Strain identifier
BacDive ID: 6224
Type strain: 
Species: Robiginitomaculum antarcticum
Strain history: <- NBRC <- K. Lee, Inha University, Incheon, Korea
NCBI tax ID(s): 1123059 (strain), 437507 (species)
version 8.1 (current version)
General
@ref: 15911
BacDive-ID: 6224
DSM-Number: 21748
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, rod-shaped
description: Robiginitomaculum antarcticum DSM 21748 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from surface seawater.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1123059 | strain |
| 437507 | species |
strain history
- @ref: 15911
- history: <- NBRC <- K. Lee, Inha University, Incheon, Korea
doi: 10.13145/bacdive6224.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Caulobacterales
- family: Hyphomonadaceae
- genus: Robiginitomaculum
- species: Robiginitomaculum antarcticum
- full scientific name: Robiginitomaculum antarcticum Lee et al. 2007
@ref: 15911
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Caulobacterales
family: Hyphomonadaceae
genus: Robiginitomaculum
species: Robiginitomaculum antarcticum
full scientific name: Robiginitomaculum antarcticum Lee et al. 2007
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32295 | negative | 2.9 µm | 0.7 µm | rod-shaped | no | |
| 69480 | negative | 99.999 |
pigmentation
- @ref: 32295
- production: yes
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_21748_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_21748_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_21748_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_21748_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_21748_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 15911
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 15911 | positive | growth | 20 | psychrophilic |
| 32295 | positive | growth | 03-25 | |
| 32295 | positive | optimum | 20 | psychrophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 32295 | positive | growth | 05-10 | alkaliphile |
| 32295 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 32295
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32295 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.999 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 32295 | NaCl | positive | growth | 0.5-5.0 % |
| 32295 | NaCl | positive | optimum | 2.25 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32295 | 16449 | alanine | + | carbon source |
| 32295 | 22653 | asparagine | + | carbon source |
| 32295 | 28260 | galactose | + | carbon source |
| 32295 | 24265 | gluconate | + | carbon source |
| 32295 | 29987 | glutamate | + | carbon source |
| 32295 | 17754 | glycerol | + | carbon source |
| 32295 | 17268 | myo-inositol | + | carbon source |
| 32295 | 18257 | ornithine | + | carbon source |
| 32295 | 26271 | proline | + | carbon source |
| 32295 | 26490 | quinate | + | carbon source |
| 32295 | 17822 | serine | + | carbon source |
| 32295 | 27082 | trehalose | + | carbon source |
| 32295 | 53423 | tween 40 | + | carbon source |
| 32295 | 53426 | tween 80 | + | carbon source |
| 32295 | 4853 | esculin | + | hydrolysis |
| 32295 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32295 | alkaline phosphatase | + | 3.1.3.1 |
| 32295 | catalase | + | 1.11.1.6 |
Isolation, sampling and environmental information
isolation
- @ref: 15911
- sample type: surface seawater
- geographic location: Maxwell Bay, King George Island, West Antarctica
- continent: Australia and Oceania
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Surface water |
taxonmaps
- @ref: 69479
- File name: preview.99_6611.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_521;96_3133;97_3837;98_4874;99_6611&stattab=map
- Last taxonomy: Robiginitomaculum antarcticum subclade
- 16S sequence: AB681940
- Sequence Identity:
- Total samples: 2295
- soil counts: 72
- aquatic counts: 2081
- animal counts: 124
- plant counts: 18
Safety information
risk assessment
- @ref: 15911
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Robiginitomaculum antarcticum gene for 16S rRNA, partial sequence, strain: NBRC 103098 | AB681940 | 1404 | ena | 437507 |
| 15911 | Robiginitomaculum antarcticum strain IMCC3195 16S ribosomal RNA gene, partial sequence | EF495229 | 1415 | ena | 437507 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Robiginitomaculum antarcticum DSM 21748 | GCA_000365025 | scaffold | ncbi | 1123059 |
| 66792 | Robiginitomaculum antarcticum DSM 21748 | 1123059.3 | wgs | patric | 1123059 |
| 66792 | Robiginitomaculum antarcticum DSM 21748 | 2522125083 | draft | img | 1123059 |
GC content
- @ref: 15911
- GC-content: 60.3
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 77.076 | yes |
| flagellated | no | 96.682 | no |
| gram-positive | no | 98.908 | yes |
| anaerobic | no | 99.191 | yes |
| aerobic | yes | 91.739 | yes |
| halophile | no | 65.793 | no |
| spore-forming | no | 97.958 | yes |
| glucose-util | yes | 80.589 | no |
| thermophile | no | 97.973 | no |
| glucose-ferment | no | 92.808 | no |
External links
@ref: 15911
culture collection no.: DSM 21748, IMCC 3195, KCCM 42687, NBRC 103098
straininfo link
- @ref: 75703
- straininfo: 400578
literature
- topic: Phylogeny
- Pubmed-ID: 17978224
- title: Robiginitomaculum antarcticum gen. nov., sp. nov., a member of the family Hyphomonadaceae, from Antarctic seawater.
- authors: Lee K, Lee HK, Choi TH, Cho JC
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.65274-0
- year: 2007
- mesh: Alphaproteobacteria/chemistry/*classification/genetics/physiology, Antarctic Regions, Bacterial Typing Techniques, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
|---|---|---|---|---|---|---|---|
| 15911 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21748) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21748 | ||||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
| 32295 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 28535 | ||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | ||
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | ||||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
| 75703 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID400578.1 | StrainInfo: A central database for resolving microbial strain identifiers |